Integrated circuits are fabricated by processing wafers with a series of wafer fabrication tools (referred to as processing tools). Each processing tool typically performs a wafer fabrication task (referred to as a process) on the wafers according to a predefined (or predetermined) process recipe that specifies various parameters of the process. For example, a deposition processing tool, such as a chemical vapor deposition (CVD) processing tool, may form a layer of the wafers within a chamber according to a deposition process recipe that specifies various parameters of the deposition process recipe, such as temperatures and pressures within the chamber as a function of time, as well as the type and flow rate of gas introduced thereto. The specified deposition process recipe may achieve a target thickness of the layer of the wafers. Typically, a fault detection and classification (FDC) system monitors the process parameters, and resulting wafer characteristics, in order to monitor conditions of the process tool. For example, if a process parameter (such as the chamber temperature or chamber pressure in a CVD processing tool) or a wafer characteristic (such as a thickness of a layer formed in the CVD processing tool) deviates from an acceptable range, the FDC system triggers an alarm so that a troubleshooting procedure can be initiated to determine whether such deviation arises from a condition of the process tool. However, it has been observed that the FDC system's monitoring function is often affected by control actions implemented (for example, by an automated process control (APC) system) to ensure that the wafer characteristics meet specified integrated circuit device targets. For example, control actions modify parameters of the predefined process recipe (such as the chamber temperature or chamber pressure of a CVD deposition process recipe) to ensure that the wafer characteristics meet the integrated circuit device targets (such as a thickness of a layer formed by the CVD processing tool). Since the FDC system monitors the process parameters and wafer characteristics that have been tuned via the control actions, a condition of the tool may thus go unnoticed, such that a tool condition may be deteriorating though wafer characteristics are meeting integrated circuit device targets. Accordingly, although existing process tool monitoring methods and systems have been generally adequate for their intended purposes, they have not been entirely satisfactory in all respects.